package kr.go.nih.biomedi.pSEVA.bean;


public class RenSeqQCFile {

	private String realFolder;
	private String inputFile;
	private String newInputFile;
	private String FieldSeparator=",";
	
	public String getRealFolder() {
		return realFolder;
	}

	public void setRealFolder(String realFolder) {
		this.realFolder = realFolder;
	}
	
	public String getInputFile() {
		return inputFile;
	}
	
	public void setInputFile(String inputFile) {
		this.inputFile = inputFile;
	}

	public String getNewInputFile() {
		return newInputFile;
	}
	
	public void setNewInputFile(String newInputFile) {
		this.newInputFile = newInputFile;
	}
	
	public String doRenOrgSeq(){
		newInputFile=inputFile.replaceAll("-", "_");
		String prinSeqCmd = "/bin/sh" + FieldSeparator + "-c" + FieldSeparator + "/bin/cp " + this.getRealFolder() + "/" + this.getInputFile() +
							" " + this.getRealFolder() + "/" + this.getNewInputFile();
		return prinSeqCmd;
		
	}
	public String doCpOrgSeq() {
		String prinSeqCmd = "/bin/sh" + FieldSeparator + "-c" + FieldSeparator + "/bin/cp " + this.getRealFolder() + "/" + this.getInputFile() + 
							" " + this.getRealFolder() + "/" + this.getInputFile() + ".org";
		return prinSeqCmd;
	}	

	public String doCpSeqQCResult() {
		String prinSeqCmd = "/bin/sh" + FieldSeparator + "-c" + FieldSeparator + "/bin/cp -f " + this.getRealFolder() + "/" + this.getNewInputFile() + 
							".good.fastq " + this.getRealFolder() + "/" + this.getInputFile();
		//String prinSeqCmd = "ls -al "+ this.getRealFolder() + "/" + this.getNewInputFile();
		return prinSeqCmd;
	}	
	
}
